[Bioperl-l] NT_xxxxx contigs file info

[Damien Mattei]

thank you i ain't got any answer since your.
Perheaps i could have find the answer in the doc but it's not really
easy to find what we want in it.I will try the NT_xxxxx contig later as 
i have enought to do already with standard genbank sequence.
Sometimes i rewrite code that perheaps
was already in bioperl,for example i spend a lot of time to write a
   perl program using Tk to display BACs and contigs graphically before
discovering bioperl-gui which althought isn't more supported , i just 
discover too gff in bioperl which could help me and i will be 
interesting in examples programs if someone have. I also want to 
contribute in bioperl but i just discover perl programming few month ago 
and i know not about perl modules and lacks time to dig in a lot.

Damien.

Jason Stajich wrote:

 > Damien - not sure if you got a satifactory answer - we can parse these
 > files in Bioperl and there is code in Bio::DB::RefSeq I believe to
 > put them back together.  However it is still not a heavily tested system
 > and probably needs someone going through it in more detail.  Part of the
 > problem is the need to assume a real Genbank or EMBL database is 
available
 > to suck in the data.
 >
 >
 >
 > On Tue, 16 Jul 2002, Damien Mattei wrote:
 >
 >
 >>is there a way in bioperl to retrieve and parse contigs
 >>such as NT_xxxxx ,for example:
 >>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NT_033929.1
 >>  to get the info on BACs assembly :
 >>CONTIG   join(AP003965.2:1..121852,AP000439.5:51986..105963,
 >>AP001824.4:7542..124888,AP001888.4:3798..161505,
 >>AP000850.4:9247..48539,AP003555.2:16283..121600,
 >>AP000879.4:2012..169725,AP002336.3:1993..112484,
 >>AP000487.5:52296..177074,AP001271.4:23675..210402,
 >>AP000590.6:22311..114287,AP001648.4:25262..166013)
 >>
 >>does someone already write something doing that or should it be?
 >>
 >>Damien
 >>
 >>-----------------------------
 >>Damien Mattei
 >>C.N.R.S / U.N.S.A - UMR 6549
 >>mailto:mattei@unice.fr
 >>http://www-iag.unice.fr/
 >>-----------------------------
 >>
 >>_______________________________________________
 >>Bioperl-l mailing list
 >>Bioperl-l@bioperl.org
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 >>
 >>
 >


-- 
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Damien Mattei
C.N.R.S / U.N.S.A - UMR 6549
Instabilite & Alterations des Genomes
Universite de Nice - Sophia Antipolis
Faculte de Medecine, Av. de Valombrose
06107 NICE Cedex 2 FRANCE
Phone: +33 (0)4 93 37 76 66
Fax:   +33 (0)4 93 53 30 71
mailto:mattei@unice.fr
http://www-iag.unice.fr/
--------------------------------------